Re: Wtrlt: Smeart out 9/3 LJ wall

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jul 15 2009 - 12:10:53 CDT

On Wed, 2009-07-15 at 14:48 +0200, Sabine Leroch wrote:
>
>
> >>> Sabine Leroch 7/13/2009 2:36 PM >>>
>
>
> Dear all

dear sabine,

> I am new to NAMD, as I found nothing related in the mailing list, I
> have to post following question. I need to simulate the adsorption of
> aminoacids in water at a graphite wall. As it is computationally very
> costly to use an atomic graphite slide, I want to represent the wall
> by a smeart out Steele 9/3 LJ potential. Is this possible with NAMD?
> If yes, how can I set the command in the input file?

not sure how to do this in detail, but my guess would be to try out
the Tcl Boundary Forces (TclBC) facility. check out the NAMD user's
guide. perhaps there may also be some examples in the NAMD tutorials
somewhere.

cheers,
   axel.

>
>
> Thank you very much
>
>
> Best regards
>
> Sabine
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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